Affymetrix (NASDAQ:AFFX)
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Affymetrix Inc. (NASDAQ:AFFX) announced today that scientists working on
the International Genome Structural Variation Consortium’s
Copy Number Variation Project have used the 500K Array to help generate
the first comprehensive copy number variation (CNV) map of the human
genome. The team discovered hundreds of CNVs that will enable
researchers to perform more powerful association studies on diseases
such as cancer, Parkinson’s and Alzheimer’s. The
results of this study have been published in the November
23, 2006 issue of Nature1 along
with a supporting paper in Genome Research2.
The study is the first publication to demonstrate the performance of
whole-genome single nucleotide polymorphism (SNP) arrays in detecting
CNVs in the general population. The Affymetrix 500K Array genotypes more
than 500,000 SNPs and offers the industry’s
highest-resolution view of CNVs in the human genome.
Researchers in the study discovered that CNVs are much more prevalent
than previously thought. CNV regions were found to comprise about 360
megabases, or around 12 percent of the human genome.
To read an Affymetrix Microarray Bulletin interview about this
study, please visit: http://microarraybulletin.com/community/article.php?p=277.
CNVs can consist of deletions, duplications or multi-site variants in
DNA segments, ranging from a few kilobases to megabases in length. They
are particularly important in genetic research because they can be
associated with specific diseases, such as an increased susceptibility
to cancer, Parkinson’s and Alzheimer’s,
as well as to conditions like HIV-1 infection and
glomerulonephritis. Certain CNVs also appear to influence drug
metabolism and increase sensitivity to particular chemical carcinogens,
which will also help to decipher the complex ways in which an individual’s
genes and the environment impact disease.
“Our results suggest that sub-microscopic
structural variants along chromosomes are more widespread than
previously thought and that researchers should study both SNPs and CNVs
when undertaking disease research,” said
Stephen Scherer, Ph.D., senior scientist in Genetics & Genome Biology at
The Hospital for Sick Children, director of The Center for Applied
Genomics and one of the lead researchers in the study.
“Our new approach will be useful in
understanding the role of copy number alteration in disease pathology.
This information should lead to the development of diagnostic tests with
sub-microscopic resolution that can detect not only mutations in cancer
but other genetic variations associated with common diseases,”
said Hiroyuki Aburatani, M.D., Ph.D., professor at the University of
Tokyo and one of the lead researchers.
“This study illustrates that in addition to
generating genotypes for over 500,000 SNPs, the Affymetrix 500K
Array enables researchers to detect more CNVs than any other available
platform. It's important to note that the combination of high-density
markers and robust analysis methods have allowed us to identify CNVs and
delineate the boundaries at a high resolution, which helps in
establishing the link between CNVs and disease pathology,”
said Keith Jones, Ph.D., vice president of molecular genetics at
Affymetrix and another of the lead researchers.
Researchers in the Nature study constructed the CNV map of the
human genome by analyzing samples from 270 people of European, Asian or
African descent, who were originally included in the International
HapMap Project. The DNA from these individuals was scanned using the
Affymetrix 500K Array and a BAC array platform developed by the Wellcome
Trust Sanger Institute. Using this combination of techniques on these
samples, the researchers discovered 1,447 CNV regions containing
hundreds of genes, disease loci, functional elements and segmental
duplications.
The other lead researchers working on the International Genome
Structural Variation Consortium’s Copy Number
Variation Project were Nigel Carter and Matthew Hurles of the Wellcome
Trust Sanger Institute and Charles Lee at the Department of Pathology at
Brigham and Women’s Hospital.
The raw data from the 500K Arrays are posted online at the Gene
Expression Omnibus (www.ncbi.nlm.nih.gov/geo).
The CNV calls have been released at the Database of Genomic Variants (http://projects.tcag.ca/variation)
together with all other data. Additional genotyping microarray-based CNV
analysis downloads can be found at the website for the Genome Science
Division RCAST, The University of Tokyo (http://www2.genome.rcast.u-tokyo.ac.jp/CNV/).
New Combined SNP/CNV Array
With more than 25 peer-reviewed publications to date, Affymetrix Human
Mapping Arrays have pioneered the utilization of whole-genome SNP arrays
for copy number analysis. Later this year, Affymetrix will introduce the
SNP 5.0 Array that was developed in collaboration with the Broad
Institute of Harvard and the Massachusetts Institute of Technology.
The new product will redefine the way association studies are performed
by assaying both SNPs and CNVs within the human population on a single
array. In addition to featuring the majority of the SNPs from the 500K
Array Set, the SNP 5.0 Array will also include 500,000 non-polymorphic
tiling probes to assess CNV in association studies.
Around 100,000 of the non-polymorphic tiling probes are specifically
targeted at approximately 2,000 previously identified CNVs, thereby
allowing future whole-genome association studies to better identify and
understand the contribution of CNVs in common diseases.
References
1Redon, R., Ishikawa, S., Fitch, K.R., Feuk,
L., Perry, G, ... Carter, N.P., Aburatani, H., Lee, C., Jones K.W.,
Scherer, S.W. and Hurles, M.E. Global variation in copy number in the
human genome. Nature. 2006 Nov 23; 444: 444-454.
2Komura, D., Shen, F., Ishikawa, S., Fitch,
K.R., Chen, W., Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles,
M.E., Lee, C., Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J. and
Aburatani, H. 2006. Genome-wide detection of human copy number
variations using high-density DNA oligonucleotide arrays. Genome Res.
2006. Advance online publication doi:10.1101/gr.5629106.
About Affymetrix
Affymetrix scientists invented the world's first high-density microarray
in 1989 and began selling the first commercial microarray in 1994. Since
then, Affymetrix GeneChip®
technology has become the industry standard in molecular biology
research. Affymetrix technology is used by the world's top
pharmaceutical, diagnostic and biotechnology companies as well as
leading academic, government and not-for-profit research institutes.
More than 1,400 systems have been installed around the world and more
than 7,000 peer-reviewed papers have been published using the
technology. Affymetrix' patented photolithographic manufacturing process
provides the most information capacity available today on an array,
enabling researchers to use a whole-genome approach to analyzing the
relationship between genetics and health. Affymetrix is headquartered in
Santa Clara, Calif., with manufacturing facilities in Sacramento,
Calif., and Bedford, Mass. The company maintains important sales and
marketing operations in Europe and Asia, and has about 1,100 employees
worldwide. For more information about Affymetrix, please visit the
company's website at www.affymetrix.com.
All statements in this press release that are not historical are
"forward-looking statements" within the meaning of Section 21E of the
Securities Exchange Act as amended, including statements regarding
Affymetrix' "expectations," "beliefs," "hopes," "intentions,"
"strategies," or the like. Such statements are subject to risks and
uncertainties that could cause actual results to differ materially for
Affymetrix from those projected, including, but not limited to: risks
and uncertainties associated with the use of the 500K Array to develop
the CNV map discussed in this press release; risks of the Company's
ability to achieve and sustain higher levels of revenue, higher gross
margins, reduced operating expenses; uncertainties relating to
technological approaches, manufacturing, product development; personnel
retention; uncertainties related to cost and pricing of Affymetrix
products; dependence on collaborative partners; uncertainties relating
to sole source suppliers; uncertainties relating to FDA and other
regulatory approvals; competition; risks relating to intellectual
property of others and the uncertainties of patent protection and
litigation. These and other risk factors are discussed in Affymetrix'
Form 10-K/A for the year ended December 31, 2005, and other SEC reports,
including its Quarterly Reports on Form 10-Q for subsequent quarterly
periods. Affymetrix expressly disclaims any obligation or undertaking to
release publicly any updates or revisions to any forward-looking
statements contained herein to reflect any change in Affymetrix'
expectations with regard thereto or any change in events, conditions or
circumstances on which any such statements are based.
NOTE: Affymetrix, the Affymetrix logo and GeneChip are registered
trademarks owned or used by Affymetrix Inc.
Affymetrix Inc. (NASDAQ:AFFX) announced today that scientists
working on the International Genome Structural Variation Consortium's
Copy Number Variation Project have used the 500K Array to help
generate the first comprehensive copy number variation (CNV) map of
the human genome. The team discovered hundreds of CNVs that will
enable researchers to perform more powerful association studies on
diseases such as cancer, Parkinson's and Alzheimer's. The results of
this study have been published in the November 23, 2006 issue of
Nature(1) along with a supporting paper in Genome Research(2).
The study is the first publication to demonstrate the performance
of whole-genome single nucleotide polymorphism (SNP) arrays in
detecting CNVs in the general population. The Affymetrix 500K Array
genotypes more than 500,000 SNPs and offers the industry's
highest-resolution view of CNVs in the human genome.
Researchers in the study discovered that CNVs are much more
prevalent than previously thought. CNV regions were found to comprise
about 360 megabases, or around 12 percent of the human genome.
To read an Affymetrix Microarray Bulletin interview about this
study, please visit:
http://microarraybulletin.com/community/article.php?p=277.
CNVs can consist of deletions, duplications or multi-site variants
in DNA segments, ranging from a few kilobases to megabases in length.
They are particularly important in genetic research because they can
be associated with specific diseases, such as an increased
susceptibility to cancer, Parkinson's and Alzheimer's, as well as to
conditions like HIV-1 infection and glomerulonephritis. Certain CNVs
also appear to influence drug metabolism and increase sensitivity to
particular chemical carcinogens, which will also help to decipher the
complex ways in which an individual's genes and the environment impact
disease.
"Our results suggest that sub-microscopic structural variants
along chromosomes are more widespread than previously thought and that
researchers should study both SNPs and CNVs when undertaking disease
research," said Stephen Scherer, Ph.D., senior scientist in Genetics &
Genome Biology at The Hospital for Sick Children, director of The
Center for Applied Genomics and one of the lead researchers in the
study.
"Our new approach will be useful in understanding the role of copy
number alteration in disease pathology. This information should lead
to the development of diagnostic tests with sub-microscopic resolution
that can detect not only mutations in cancer but other genetic
variations associated with common diseases," said Hiroyuki Aburatani,
M.D., Ph.D., professor at the University of Tokyo and one of the lead
researchers.
"This study illustrates that in addition to generating genotypes
for over 500,000 SNPs, the Affymetrix 500K Array enables researchers
to detect more CNVs than any other available platform. It's important
to note that the combination of high-density markers and robust
analysis methods have allowed us to identify CNVs and delineate the
boundaries at a high resolution, which helps in establishing the link
between CNVs and disease pathology," said Keith Jones, Ph.D., vice
president of molecular genetics at Affymetrix and another of the lead
researchers.
Researchers in the Nature study constructed the CNV map of the
human genome by analyzing samples from 270 people of European, Asian
or African descent, who were originally included in the International
HapMap Project. The DNA from these individuals was scanned using the
Affymetrix 500K Array and a BAC array platform developed by the
Wellcome Trust Sanger Institute. Using this combination of techniques
on these samples, the researchers discovered 1,447 CNV regions
containing hundreds of genes, disease loci, functional elements and
segmental duplications.
The other lead researchers working on the International Genome
Structural Variation Consortium's Copy Number Variation Project were
Nigel Carter and Matthew Hurles of the Wellcome Trust Sanger Institute
and Charles Lee at the Department of Pathology at Brigham and Women's
Hospital.
The raw data from the 500K Arrays are posted online at the Gene
Expression Omnibus (www.ncbi.nlm.nih.gov/geo). The CNV calls have been
released at the Database of Genomic Variants
(http://projects.tcag.ca/variation) together with all other data.
Additional genotyping microarray-based CNV analysis downloads can be
found at the website for the Genome Science Division RCAST, The
University of Tokyo (http://www2.genome.rcast.u-tokyo.ac.jp/CNV/).
New Combined SNP/CNV Array
With more than 25 peer-reviewed publications to date, Affymetrix
Human Mapping Arrays have pioneered the utilization of whole-genome
SNP arrays for copy number analysis. Later this year, Affymetrix will
introduce the SNP 5.0 Array that was developed in collaboration with
the Broad Institute of Harvard and the Massachusetts Institute of
Technology.
The new product will redefine the way association studies are
performed by assaying both SNPs and CNVs within the human population
on a single array. In addition to featuring the majority of the SNPs
from the 500K Array Set, the SNP 5.0 Array will also include 500,000
non-polymorphic tiling probes to assess CNV in association studies.
Around 100,000 of the non-polymorphic tiling probes are
specifically targeted at approximately 2,000 previously identified
CNVs, thereby allowing future whole-genome association studies to
better identify and understand the contribution of CNVs in common
diseases.
References
(1) Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G, ...
Carter, N.P., Aburatani, H., Lee, C., Jones K.W., Scherer, S.W. and
Hurles, M.E. Global variation in copy number in the human genome.
Nature. 2006 Nov 23; 444: 444-454.
(2) Komura, D., Shen, F., Ishikawa, S., Fitch, K.R., Chen, W.,
Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles, M.E., Lee, C.,
Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J. and Aburatani, H.
2006. Genome-wide detection of human copy number variations using
high-density DNA oligonucleotide arrays. Genome Res. 2006. Advance
online publication doi:10.1101/gr.5629106.
About Affymetrix
Affymetrix scientists invented the world's first high-density
microarray in 1989 and began selling the first commercial microarray
in 1994. Since then, Affymetrix GeneChip(R) technology has become the
industry standard in molecular biology research. Affymetrix technology
is used by the world's top pharmaceutical, diagnostic and
biotechnology companies as well as leading academic, government and
not-for-profit research institutes. More than 1,400 systems have been
installed around the world and more than 7,000 peer-reviewed papers
have been published using the technology. Affymetrix' patented
photolithographic manufacturing process provides the most information
capacity available today on an array, enabling researchers to use a
whole-genome approach to analyzing the relationship between genetics
and health. Affymetrix is headquartered in Santa Clara, Calif., with
manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The
company maintains important sales and marketing operations in Europe
and Asia, and has about 1,100 employees worldwide. For more
information about Affymetrix, please visit the company's website at
www.affymetrix.com.
All statements in this press release that are not historical are
"forward-looking statements" within the meaning of Section 21E of the
Securities Exchange Act as amended, including statements regarding
Affymetrix' "expectations," "beliefs," "hopes," "intentions,"
"strategies," or the like. Such statements are subject to risks and
uncertainties that could cause actual results to differ materially for
Affymetrix from those projected, including, but not limited to: risks
and uncertainties associated with the use of the 500K Array to develop
the CNV map discussed in this press release; risks of the Company's
ability to achieve and sustain higher levels of revenue, higher gross
margins, reduced operating expenses; uncertainties relating to
technological approaches, manufacturing, product development;
personnel retention; uncertainties related to cost and pricing of
Affymetrix products; dependence on collaborative partners;
uncertainties relating to sole source suppliers; uncertainties
relating to FDA and other regulatory approvals; competition; risks
relating to intellectual property of others and the uncertainties of
patent protection and litigation. These and other risk factors are
discussed in Affymetrix' Form 10-K/A for the year ended December 31,
2005, and other SEC reports, including its Quarterly Reports on Form
10-Q for subsequent quarterly periods. Affymetrix expressly disclaims
any obligation or undertaking to release publicly any updates or
revisions to any forward-looking statements contained herein to
reflect any change in Affymetrix' expectations with regard thereto or
any change in events, conditions or circumstances on which any such
statements are based.
NOTE: Affymetrix, the Affymetrix logo and GeneChip are registered
trademarks owned or used by Affymetrix Inc.